REDH: A database of RNA editome in hematopoietic differentiation and malignancy.
REDH: A database of RNA editome in hematopoietic differentiation and malignancy.
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DOI：
10.1097/cm9.0000000000002782
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发表时间：
2024-02-05
影响因子：
6.1
通讯作者：
中科院分区：
文献类型：
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作者：
通过脱氨作用将腺苷(A)转化为肌苷(I)是RNA编辑的主要形式，影响了各种真核生物物种的许多核和细胞质转录物。数以百万计的高置信度RNA编辑位点已被识别并整合到各种RNA数据库中，为快速识别癌症的关键驱动因素和潜在的治疗靶点提供了方便的平台。然而，在造血细胞和造血恶性肿瘤中整合RNA编辑的可用数据库仍然缺乏。我们从美国国家生物技术信息中心（NCBI）基因表达综合数据库（GEO）下载了29例白血病患者和19例健康供者的RNA测序（RNA-seq）数据，并使用了我们之前研究获得的12个小鼠造血细胞群的RNA-seq数据。我们进行了序列比对，确定了RNA编辑位点，并获得了与正常造血发育相关的特征性编辑位点和与血液病相关的异常编辑位点。我们建立了一个新的数据库“REDH”，代表RNA编辑组在造血分化和恶性肿瘤中的作用。REDH是一个精心策划的RNA编辑组与造血之间关联的数据库。REDH整合了来自12个小鼠成年造血细胞群的30,796个编辑位点，并系统地表征了来自48个队列（人类）的恶性造血样本中的400,000多个编辑事件。通过分化（Differentiation）、疾病（Disease）、富集（Enrichment）和知识（knowledge）模块，系统整合每个A-to-I编辑位点，包括其在整个基因组中的分布、临床信息（人类样本）以及生理和病理条件下的功能编辑位点。此外，REDH还比较了不同血液恶性肿瘤和健康对照之间编辑位点的异同。REDH可以访问http://www.redhdatabase.com/。这个用户友好的数据库将有助于理解RNA编辑在造血分化和恶性肿瘤中的机制。它提供了一组与维持造血稳态和确定恶性肿瘤的潜在治疗靶点有关的数据。
The conversion of adenosine (A) to inosine (I) through deamination is the prevailing form of RNA editing, impacting numerous nuclear and cytoplasmic transcripts across various eukaryotic species. Millions of high-confidence RNA editing sites have been identified and integrated into various RNA databases, providing a convenient platform for the rapid identification of key drivers of cancer and potential therapeutic targets. However, the available database for integration of RNA editing in hematopoietic cells and hematopoietic malignancies is still lacking. We downloaded RNA sequencing (RNA-seq) data of 29 leukemia patients and 19 healthy donors from National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database, and RNA-seq data of 12 mouse hematopoietic cell populations obtained from our previous research were also used. We performed sequence alignment, identified RNA editing sites, and obtained characteristic editing sites related to normal hematopoietic development and abnormal editing sites associated with hematologic diseases. We established a new database, "REDH", represents RNA editome in hematopoietic differentiation and malignancy. REDH is a curated database of associations between RNA editome and hematopoiesis. REDH integrates 30,796 editing sites from 12 murine adult hematopoietic cell populations and systematically characterizes more than 400,000 edited events in malignant hematopoietic samples from 48 cohorts (human). Through the Differentiation, Disease, Enrichment, and knowledge modules, each A-to-I editing site is systematically integrated, including its distribution throughout the genome, its clinical information (human sample), and functional editing sites under physiological and pathological conditions. Furthermore, REDH compares the similarities and differences of editing sites between different hematologic malignancies and healthy control. REDH is accessible at http://www.redhdatabase.com/. This user-friendly database would aid in understanding the mechanisms of RNA editing in hematopoietic differentiation and malignancies. It provides a set of data related to the maintenance of hematopoietic homeostasis and identifying potential therapeutic targets in malignancies.
影响因子：
3.7
作者：
Maas, Stefan;Gommans, Willemijn M.
通讯作者：
Gommans, Willemijn M.